Testing budget photosystems to reach an optimal solution for the herbarium digitization purposes
PDF

Keywords

herbarium digitization
image quality assessment
photosystems
delta E
color accuracy

How to Cite

Novikov, A., Sup-Novikova, M., Nachychko, V., & Kuzyarin, O. (2023). Testing budget photosystems to reach an optimal solution for the herbarium digitization purposes. Plant Introduction, (99-100), 36-50. https://doi.org/10.46341/PI2023010

Abstract

The current paper stresses the application of different budget photosystems for digitization of herbarium specimens. Twelve photosystems were compared by color accuracy reproduction of the images. It was found that the photosystem built on the basis of photocamera Canon EOS 800D and fixed lens Tokina AT-X M35 PRO DX AF 35 mm f/2.8 Macro and currently used for the digitization of the LWS herbarium collection demonstrated the best results among other tested photosystems. It also produced the images with the same or even better color accuracy as in images downloaded from P, PI, B, and W virtual herbaria. Nevertheless, its color accuracy measured as ΔE2000, in general, does not meet recent criteria ascertained for the herbarium digitization purposes and new FADGI’s requirements. This photosystem has been found to have improving potential and, hence, should be optimized. On the other hand, it was also shown that smartphone Samsung Galaxy S10 could produce images with the same or even better color accuracy compared to some images deposited at P, PI, W, and B virtual herbaria. Therefore, in conditions of extreme situations and hostilities, such smartphones with additional external illumination can serve for urgent digitization of natural history collections. Finally, we doubt the application of commonly used color targets for the digitization of herbariaum preserved specimens since the original living color of such specimens is usually lost during conservation and preservation. Instead, it would be more beneficial to apply advanced targets to evaluate the spatial accuracy of images since they can incorrectly represent the important morphological characters of preserved specimens.

https://doi.org/10.46341/PI2023010
PDF

References

Baratè, A., Caccianiga, M., Caporali, E., Ludovico, L.A., Pinto, S., Presti, G., Sala, E., & Testa, A. (2020). Preserving and promoting the herbarium of the University of Milan through digital technologies. IOP Conference Series: Materials Science and Engineering, 949(1), Article 012066. https://doi.org/10.1088/1757-899X/949/1/012066

Carta, A., Fernández-Pascual, E., Gioria, M., Müller, J.V., Rivière, S., Rosbakh, S., Saatkamp, A., Vandelook, F. & Mattana, E. (2022). Climate shapes the seed germination niche of temperate flowering plants: a meta-analysis of European seed conservation data. Annals of Botany, 129(7), 775–786. https://doi.org/10.1093/aob/mcac037

Davis, C.C. (2023). The herbarium of the future. Trends in Ecology & Evolution, 38(5), 412–423. https://doi.org/10.1016/j.tree.2022.11.015

Dawson-Glass, E., & Hargreaves, A.L. (2022). Does pollen limitation limit plant ranges? Evidence and implications. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1846), Article 20210014. https://doi.org/10.1098/rstb.2021.0014

Drew, J.A., Moreau, C.S., & Stiassny, M.L. (2017). Digitization of museum collections holds the potential to enhance researcher diversity. Nature Ecology & Evolution, 1(12), 1789–1790. https://doi.org/10.1038/s41559-017-0401-6

DT Heritage. (2023). Overview of FADGI & METAMORFOZE. DT Heritage. https://heritage-digitaltransitions.com/digitization-program-planning/overview-of-fadgi-metamorfoze-guidelines/

Gries, C., Gilbert, M.E.E., & Franz, N.M. (2014). Symbiota – a virtual platform for creating voucher-based biodiversity information communities. Biodiversity Data Journal, 2, Article e1114. https://doi.org/10.3897/BDJ.2.e1114

Gu, K., Liu, H., & Zhou, C. (2022). Quality assessment of enhanced images. In K. Gu, H. Liu, & C. Zhou, Quality Assessment of Visual Content (pp. 127–163). Springer Singapore. https://doi.org/10.1007/978-981-19-3347-9_5

Hammer, Ø., Harper, D.A.T., & Ryan, P.D. (2001). PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4(1), Article 4. http://palaeo-electronica.org/2001_1/past/issue1_01.htm

Harris, K.M., & Marsico, T.D. (2017). Digitizing specimens in a small herbarium: a viable workflow for collections working with limited resources. Applications in Plant Sciences, 5(4), Article 1600125. https://doi.org/10.3732/apps.1600125

Hasler, D., & Suesstrunk, S. (2003). Measuring color fulness in natural images. Proceedings of SPIE, 5007, 87–95. https://doi.org/10.1117/12.477378

Hedrick, B.P., Heberling, J.M., Meineke, E.K., Turner, K.G., Grassa, C.J., Park, D.S., Kennedy, J., Clarke, J.A., Cook, J.A., Blackburn, D.C., Edwards, S.V., & Davis, C.C. (2020). Digitization and the future of natural history collections. BioScience, 70(3), 243–251. https://doi.org/10.1093/biosci/biz163

Hussein, B.R., Malik, O.A., Ong, W.-H., & Slik, J.W.F. (2022). Applications of computer vision and machine learning techniques for digitized herbarium specimens: a systematic literature review. Ecological Informatics, 69, Article 101641. https://doi.org/10.1016/j.ecoinf.2022.101641

iDigBio. (2014). iDigBio imaging equipment recommendations. Ver. 2.0. iDigBio White Papers. University of Florida. https://www.idigbio.org/wiki/images/8/86/IDigBioImagingGeneralEquipmentRecommendations1_0.pdf

Jackowiak, B., Lawenda, M., Nowak, M.M., Wolniewicz, P., Błoszyk, J., Urbaniak, M., Szkudlarz, P., Jędrasiak, D., Wiland-Szymańska, J., Bajaczyk, R., & Meyer, N. (2022). Open access to the digital biodiversity database: a comprehensive functional model of the natural history collections. Diversity, 14(8), Article 596. https://doi.org/10.3390/d14080596

Khan, N., Thelwall, M., & Kousha, K. (2021). Measuring the impact of biodiversity datasets: data reuse, citations and altmetrics. Scientometrics, 126, 3621–3639. https://doi.org/10.1007/s11192-021-03890-6

Le Page, M. (2022, May 19). Priceless samples from Ukraine’s seed bank destroyed in bomb attack. New Scientist. https://www.newscientist.com/article/2321008-priceless-samples-from-ukraines-seed-bank-destroyed-in-bomb-attack/

Mosyakin, S.L., & Shiyan, N.M. (2022). The M.G. Kholodny Institute of Botany and the National Herbarium of Ukraine (KW), Kyiv: Damage due to the missile strikes on 10 October 2022. Ukrainian Botanical Journal, 79(5), 339–342. https://ukrbotj.co.ua/pdf/79/5/ukrbotj-2022-79-5-339.pdf

Nelson, G. & Ellis, S. (2019). The history and impact of digitization and digital data mobilization on biodiversity research. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1763), Article 20170391. https://doi.org/10.1098/rstb.2017.0391

Nieva de la Hidalga, A., Rosin, P.L., Sun, X., Bogaerts, A., De Meeter, N., De Smedt, S., Strack van Schijndel, M., Van Wambeke, P., & Groom, Q. (2020). Designing an herbarium digitisation workflow with built-in image quality management. Biodiversity Data Journal, 8, Article e47051. https://doi.org/10.3897/BDJ.8.e47051

Novikov, A. (2019, November 27–29). Digitization of natural collections – the way to immortality. In Abstracts of the 14th International Young Scientists’ Conference “Biology: From a Molecule Up to the Biosphere” (pp. 12–14). V.N. Karazin Kharkiv National University. https://doi.org/10.5281/zenodo.3594474

Novikov, A., & Sup-Novikova, M. (2021). Simple and cheap photosystem for herbarium digitization. Plant Introduction, 91/92, 50–53. https://doi.org/10.46341/PI2021015

Novikov, A.V., Hushtan, H.H.,Hushtan, K.V., Kuzyarin, O.T., Leleka, D.Y., Nachychko, V.O., Prots, B.H., Rizun, V.B., Savytska, A.G., Susulovska, S.A., & Susulovsky, A.S. (2023). Outlining the aims and format of the project “Digitisation of natural history collections damaged as a result of hostilities and related factors: development of protocols and implementation based on the State Museum of Natural History of the National Academy of Sciences of Ukraine”. Scientific Proceedings of the State Museum of Natural History of the National Academy of Sciences of Ukraine, 39, 19–30. (In Ukrainian). https://doi.org/10.36885/nzdpm.2023.39.19-30

Palus, H. (2006). Colorfulness of the image: definition, computation, and properties. Proceedings of SPIE, 6158, Article 615805. https://doi.org/10.1117/12.675760

Pavlyshyn, O. (2022, June 01). What happened to the only Ukrainian genetic bank of plants. Kunsht. (In Ukrainian). https://kunsht.com.ua/articles/shho-naspravdi-stalosya-z-yedinim-v-ukraini-genetichnim-bankom-roslin

Picturae. (2023). Delt.ae. Picturae. https://deltae.picturae.com/

Rieger, T. (Ed.). (2016). Technical guidelines for digitizing cultural heritage materials: creation of raster image files. Federal Agencies Digitization Guidelines Initiative, USA. https://www.digitizationguidelines.gov/guidelines/FADGI%20Federal%20%20Agencies%20Digital%20Guidelines%20Initiative-2016%20Final_rev1.pdf

Rieger, T., Phelps, K.A., Beckerle, H., Brown, T., Frederick, R., Mitrani, S., Breen, P., Breitbart, M., Williams, D., Triplett, R., & Horsley, M. (2023). Technical guidelines for digitizing cultural heritage materials (3rd ed.). Federal Agencies Digitization Guidelines Initiative, USA. https://www.digitizationguidelines.gov/guidelines/FADGI%20Technical%20Guidelines%20for%20Digitizing%20Cultural%20Heritage%20Materials_3rd%20Edition_05092023.pdf

Samain, M.-S., Guzmán Díaz, S., Machuca Machuca, K., Dolores Fuentes, A.C., Zacarías Correa, A.G., Valentín Martínez, D., Aldaba Núñez, F.A., Redonda-Martínez, R., Oldfield, S.F., & Martínez Salas, E.M. (2023). Meta-analysis of Red List conservation assessments of Mexican endemic and near endemic tree species shows nearly two thirds of these are threatened. Plants, People, Planet, 5(4), 581–599. https://doi.org/10.1002/ppp3.10308

Schindel, D.E., & Cook, J.A. (2018). The next generation of natural history collections. PLOS Biology, 16(7), Article e2006125. https://doi.org/10.1371/journal.pbio.2006125

Takano, A., Horiuchi, Y., Fujimoto, Y., Aoki, K., Mitsuhashi, H., & Takahashi, A. (2019). Simple but long-lasting: a specimen imaging method applicable for small- and medium-sized herbaria. PhytoKeys, 118, 1–14. https://doi.org/10.3897/phytokeys.118.29434

Thiers, B.M. (2023). The world’s herbaria 2022: A summary report based on data from Index Herbariorum, Issue 6.0. New York Botanical Garden. https://sweetgum.nybg.org/science/wp-content/uploads/2023/10/The_Worlds_Herbaria_2022_Report.docx

Vajda, V., McLoughlin, S., & Shevchuk, O. (2022, June 19–20). The war in Ukraine – Its impact on palaeobotany, palynology, herbaria and museums. In S. McLoughlin (Ed.), 11th European Palaeobotany and Palynology Conference Abstracts, Program and Proceedings (pp. 75–76). Swedish Museum of Natural History.

van Dormolen, H. (2012). Metamorfoze preservation imaging guidelines: Image quality, version 1.0, January 2012. Koninklijke Bibliotheek. https://www.metamorfoze.nl/sites/default/files/documents/Metamorfoze_Preservation_Imaging_Guidelines_1.0.pdf

van Dormolen, H. (2019, May 14–17). Metamorfoze preservation imaging guidelines, version 2.0. In Proceedings of the IS&T Conference “Archiving 2019” (pp. 9–11). Society for Imaging Science and Technology. https://doi.org/10.2352/issn.2168-3204.2019.1.0.3

Zerman, E., Rana, A., & Smolic, A. (2019, September 22–25). Colornet – estimating colorfulness in natural images. In Proceedings of the 2019 IEEE International Conference on Image Processing (ICIP) (pp. 3791–3795). Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/ICIP.2019.8803407

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Downloads

Download data is not yet available.